Alta-Cyclic specifications

Information


Unique identifier OMICS_01149
Name Alta-Cyclic
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format INT with Bustard reads
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Version 0.2.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yaniv Erlich <>

Publication for Alta-Cyclic

Alta-Cyclic in publications

 (2)
PMCID: 3141275
PMID: 21576222
DOI: 10.1093/nar/gkr344

[…] efforts have been made to improve the error rate of the illumina sequencers. besides the improvement in experimental procedures, several base call programs have been developed. these include ibis, alta-cyclic and rolexa (,,). these programs consider a simple model for the regression of quality and improve base calls in terms of mismatch ratio. we examined the ibis base calls for phix and found […]

PMCID: 3178052
PMID: 21245079
DOI: 10.1093/bib/bbq077

[…] implemented in bustard can be found in []., within the last 2 years, numerous papers have been published which improve upon the native base-calling implementation. the first among them which was alta-cyclic. alta-cyclic uses a parametric model for dephasing and then corrects for cross-talk using a cycle dependent cross-talk matrix. support vector machines (svm) are used to determine the base […]


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Alta-Cyclic institution(s)
Watson School of Biological Sciences, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
Alta-Cyclic funding source(s)
Supported by grants from the US National Institute of Health, the National Science Foundation and the Stanley Foundation.

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